Mapping the morphological identifiers of distinct conformations via the protein translocation current in nanopores

Nanoscale ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 6053-6065
Author(s):  
Mingkun Zhang ◽  
Shenbao Chen ◽  
Jinrong Hu ◽  
Qihan Ding ◽  
Linda Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Translocation ◽  
Theoretical Method ◽  
Protein Conformations ◽  
Dynamics Simulations

A theoretical method based on molecular dynamics simulations was proposed to resolve the morphological signatures of protein conformations by orientation-modulated principle in nanopore sensing technique.

scholarly journals Fast leaps between millisecond confinements govern Ase1 diffusion along microtubules

2021 ◽  
Author(s):  
Łukasz Bujak ◽  
Kristýna Holanová ◽  
Antonio García Marín ◽  
Verena Henrichs ◽  
Ivan Barvík ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cell Division ◽  
Molecular Dynamics Simulations ◽  
Interaction Potential ◽  
Electrostatic Potential ◽  
Fundamental Mode ◽  
Protein Translocation ◽  
Periodic Surface ◽  
Tubulin Dimer ◽  
Dynamics Simulations

AbstractDiffusion is the most fundamental mode of protein translocation within cells. Confined diffusion of proteins along the electrostatic potential constituted by the surface of microtubules, although modeled meticulously in molecular dynamics simulations, has not been experimentally observed in real-time. Here, we used interferometric scattering microscopy to directly visualize the movement of the microtubule-associated protein Ase1 along the microtubule surface at nanometer and microsecond resolution. We resolved millisecond confinements of Ase1 and fast leaps between these positions of dwelling preferentially occurring along the microtubule protofilaments, revealing Ase1’s mode of diffusive translocation along the microtubule’s periodic surface. The derived interaction potential closely matches the tubulin-dimer periodicity and the distribution of the electrostatic potential on the microtubule lattice. We anticipate that mapping the interaction landscapes for different proteins on microtubules, finding plausible energetic barriers of different positioning and heights, will provide valuable insights into regulating the dynamics of essential cytoskeletal processes, such as intracellular cargo trafficking, cell division, and morphogenesis, all of which rely on diffusive translocation of proteins along microtubules.

Tight knots in proteins: can they block the mitochondrial pores?

2013 ◽  
Vol 41 (2) ◽  
pp. 620-624 ◽  
Author(s):  
Piotr Szymczak
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Present Article ◽  
Protein Translocation ◽  
Cellular Membranes ◽  
Numerical Studies ◽  
Knotted Protein ◽  
Knotted Proteins ◽  
Dynamics Simulations

Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process since the diameter of the pore is smaller than the size of maximally tightened knot. In the present article, I briefly review the experimental and numerical studies of tight knots in proteins, with a particular emphasis on the estimates of the size of these knots. Next, I discuss the process of protein translocation through the mitochondrial pores and report the results of molecular dynamics simulations of knotted protein translocation, which show how the knot can indeed block the pore.

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